I have been reading all the posts about signing 3do isos and decided to try and sign the Orbatak iso using the Game guru files as mentioned in the guide on the site here. It seems straight forward enough but I'm confused as to how and where I type in the '3DOEncrypt generomtags isoname.iso' part.
I have no idea what to do next so and help would be appreciated.

If you are in windows you can make a batch file (for example encrypt.bat)
which you open with a text editor and type the single line and save:
3doEncrypt.exe genromtags file.iso
You will need to have the 3doEncrypt.exe tool of course at the same folder as the iso.